Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, United States of America.

Abstract

The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins.

Manhattan plots of autozygosity were generated using the FL values (y-axis) for each SNP locus relative to its genome coordinate (x-axis; Chr indicated) for A) Group I, B) Group II-A, and C) Group II-B. The grey horizintal line indicates the threshold for FL > 0.16, which represents approximately the top 2.5% of autozygosity detected.

Manhattan plots of comparative autozygosity were generated using –log10p of chi-square tests between two groups (y-axis) for each SNP locus relative to its genome coordinate (x-axis; Chr indicated) for A) Group II-A versus I, B) Group II-B versus I, and C) Group II-A versus II-B.